SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Mixing libraries with different insert lengths in a lane MesutOezil Illumina/Solexa 4 04-22-2013 12:37 PM
multiple exons aligned to assemblies Lu Zheng Illumina/Solexa 2 09-25-2012 08:13 AM
tophat/cufflinks with different read lengths libraries linsson RNA Sequencing 0 07-03-2012 11:21 AM
Help! SNP determination across multiple assemblies austic Bioinformatics 4 02-28-2012 08:37 AM
Multiple fragment lengths in single 454 titanium run? Tom McFarland 454 Pyrosequencing 3 05-18-2011 07:47 AM

Reply
 
Thread Tools
Old 06-23-2017, 10:57 AM   #1
samche42
Junior Member
 
Location: South Africa

Join Date: Jun 2017
Posts: 2
Question Multiple libraries of different lengths - single or seperate assemblies?

Hi!

I have three Ion torrent libraries; a 600bp, 400bp and a 200bp library. I intend to use SPAdes to assemble the reads into contigs but am unsure whether I can use three different sized libraries in a single assembly? (As I'm pretty sure it's going to have an affect on the optimal k-mer value).

Has anyone used various read sizes in a single assembly or would it be wiser to assemble one library at a time and use the resultant contigs from the first assembly as "untrusted contigs" in the next assembly and so on?

Any advice would be massively appreciated!!
samche42 is offline   Reply With Quote
Old 06-27-2017, 12:05 PM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,695
Default

SPAdes documentation seems to indicate that the distribution of insert size is important to some of its heuristics, but I think coverage is more important... also it's a multi-kmer assembler so you don't need a single ideal kmer length. I normally run with K=25,55,95,125. I'd just feed them all into SPAdes.
Brian Bushnell is offline   Reply With Quote
Old 06-27-2017, 01:06 PM   #3
samche42
Junior Member
 
Location: South Africa

Join Date: Jun 2017
Posts: 2
Default

Ok brilliant - Thanks Brian
samche42 is offline   Reply With Quote
Reply

Tags
assembly, ion torrent, read length, spades

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:38 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO